Methods and systems of extracting extensible motifs from a sequence include assigning a significance to extensible motifs within the sequence based upon a syntactic and statistical analysis, and identifying extensible motifs having a significance that exceeds a predetermined threshold.
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1. A method of extracting an extensible motif from a sequence, said method comprising: on a processing unit of a computer, assigning a significance, comprising an extensible z-score, to an extensible motif within said sequence based upon a syntactic and statistical analysis; and identifying an extensible motif having a significance that exceeds a predetermined threshold, wherein said assigning said significance comprises restricting a computation of the extensible z-score for each of said motifs to classes of maximal motifs.
2. The method of claim 1 , wherein said restricting said computation of the extensible z-score comprises: pairwise iterating combinations of segments within said sequence to identify a maximal extensible motif; and pruning a maximal extensible motif which is not viable.
3. The method of claim 1 , wherein said assigning said significance comprises: scanning the sequence to identify patterns that have two solid characters; storing start and end positions of the identified patterns; and combining all cells with a dot character and the same start and end solid characters to construct extensible cells.
4. The method of claim 1 , wherein said assigning said significance comprises pruning by occurrences.
5. The method of claim 1 , wherein said assigning said significance comprises pruning by composition.
6. A system for extracting an extensible motif from a sequence, said system comprising: means for assigning a significance, comprising an extensible z-score, to an extensible motif within said sequence based upon a syntactic and statistical analysis; and means for identifying an extensible motif having a significance that exceeds a predetermined threshold, wherein said means for assigning said significance comprises means for restricting a computation of the extensible z-score for each of said motifs to classes of maximal motifs.
7. The system of claim 6 , wherein said means for restricting said computation of the extensible z-score comprises: means for pairwise iterating combinations of segments within said sequence to identify a maximal extensible motif; and means for pruning a maximal extensible motif which is not viable.
8. The system of claim 6 , wherein said means for assigning said significance comprises: means for scanning the sequence to identify patterns that have two solid characters; means for storing start and end positions of the identified patterns; and means for combining all cells with a dot character and a same start and end solid characters to construct extensible cells.
9. The system of claim 6 , wherein said means for assigning said significance comprises pruning by occurrences.
10. The system of claim 6 , wherein said means for assigning said significance comprises pruning by composition.
11. The method of claim 1 , wherein said extensible motif comprises at least one annotated dot character.
12. The method of claim 1 , further comprising displaying a list of identified extensible motifs.
13. The method of claim 12 , further comprising displaying statistical information for each of said displayed extensible motifs.
14. The method of claim 1 , further comprising iterating said assigning said significance and said identifying said extensible motif.
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September 15, 2010
October 16, 2012
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